This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The long standing workhorse of mass spectrometry based peptide sequence analyses and identifications is undoubtedly the use of collision induced dissociation (CID) for fragmentation analysis. However, the recent widespread availability of the alternative fragmentation method Electron Transfer Dissociation (ETD) has prompted many researchers to explore the capabilities and limitations of this approach. ETD fragmentation yields different fragment ion types and follows different rules to CID, rendering reliable interpretation of data somewhat challenging for existing analysis softwares. In this study, being performed by the Proteome Informatics Research Group of the Association of Biomolecular Resource Facilities, the ability of existing algorithms to reliably identify ETD spectra of peptides from a common dataset is being assessed. The reference dataset will be partly acquired within the UCSF Mass Spectrometry Facility and the Facility's expertise will be used to assist in the interpretation of the results of the study. The results will be used to catalyze the further improvement of software tools available to the research community for interpretation of peptide ETD MS/MS spectra.